I think it's too early to say that he 'disrupts the quality of the franchise.' They can still incorporate Batman and have it still be a proper, character-driven Superman movie.
However, it would have to involve making Batman a minor character who isn't likeable at first. Also, their natural love for the Batman character might override their intentions.

I honestly feel like Superman:TAS did a lot of stuff right, it just didn't have the "organic" quality of BTAS because the creators liked the Knight more. This becomes especially obvious in the "World's Finest" episode.